gprofiler-official

What it is and what it does

gprofiler-official is the official Python 3 client for the g:Profiler toolkit, a web-based bioinformatics platform for functional analysis. It provides three main tools: g:GOSt (profile) performs enrichment analysis to identify statistically significant functional terms and gene annotations in your query; g:Convert maps gene identifiers between different namespaces (HGNC, Entrez, UniProt, etc.); and g:Orth finds orthologous genes in related organisms. The library communicates with the g:Profiler backend via requests and can optionally return results as pandas DataFrames.

The package is designed for researchers analyzing gene lists from experiments or computational predictions. It abstracts away HTTP communication and result parsing, letting you work directly with Python objects or structured data. The 1.0.x release introduced breaking API changes from the 0.3.x series, so existing code may require migration.

Use it for:

• Identify enriched Gene Ontology terms and biological pathways in a list of differentially expressed genes from RNA-seq.
• Convert gene symbols to Entrez Gene IDs or other identifier systems for cross-database lookups.
• Map human genes to their mouse orthologs for translating findings between model organisms.
• Batch-process multiple gene lists with different enrichment parameters and combine results programmatically.
• Integrate functional annotation into automated bioinformatics pipelines without manual web interface interaction.

Worth the install?

AI-flagged interpretation of the facts on this page — verify before relying

Python interface to g:Profiler toolkit for functional enrichment analysis, gene identifier conversion, and ortholog mapping across organisms.

Yes, if you need functional enrichment analysis and the g:Profiler backend remains operational. The low install friction and permissive license are favorable. However, the package is abandoned (last release 2019-04-02) and you should verify that the upstream g:Profiler service itself is still maintained and accessible before committing to a production workflow. No known security vulnerabilities.

Install

gprofiler-official on PyPI

pip install gprofiler-official

uv add gprofiler-official

poetry add gprofiler-official

Installing gprofiler-official

Before you install

Low install friction with a single runtime dependency (requests). However, the package is abandoned—last release was 2019-04-02, over 2691 days ago. No recent maintenance or updates are available.

License in practice

Licensed under BSD (permissive), which allows commercial and private use with minimal restrictions.

Quickstart

pip install gprofiler-official

from gprofiler import GProfiler

gp = GProfiler(return_dataframe=True)
results = gp.profile(organism='hsapiens', query=['NR1H4', 'TRIP12', 'UBC'])

Requires the g:Profiler backend service to be accessible; no local fallback. Optional pandas dependency for DataFrame output.

Verify before relying

• Whether the g:Profiler backend service remains operational and maintained independently of this client library.
• Compatibility with current Python 3 versions and whether breaking API changes in 1.0.x remain the only documented incompatibility.
• Whether pandas integration (mentioned as optional) is still functional or requires workarounds.

Package facts

Evidence: gprofiler_official-1.0.0-py3-none-any.whl

Tags

More Bio-Informatics packages